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JonJala / mtag

Python command line tool for Multi-Trait Analysis of GWAS (MTAG)
GNU General Public License v3.0
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Problem with missing freq column #83

Open chenming9453 opened 4 years ago

chenming9453 commented 4 years ago

Hi all,

My summary data lacked the maf column. When I tried to run mtag. I got the following error:

Traceback (most recent call last): File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1567, in mtag(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1336, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 294, in load_and_merge_data raise IOError("--maf_min is specified but maf column is not present in sumstats {}".format(p+1)) IOError: --maf_min is specified but maf column is not present in sumstats 2

I am wondering if the maf column is necessary for mtag? I did not find any flag to avoid using maf.

Best, Ming

paturley commented 4 years ago

MTAG does require the MAF column, but you can use allele frequencies from a reference panel if you'd like.

On Sun, Nov 17, 2019 at 10:00 PM chenming9453 notifications@github.com wrote:

Hi all,

My summary data lacked the maf column. When I tried to run mtag. I got the following error:

Traceback (most recent call last): File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1567, in mtag(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 1336, in mtag DATA_U, DATA, args = load_and_merge_data(args) File "/ysm-gpfs/pi/zhao/mc2792/software/mtag/mtag.py", line 294, in load_and_merge_data raise IOError("--maf_min is specified but maf column is not present in sumstats {}".format(p+1)) IOError: --maf_min is specified but maf column is not present in sumstats 2

I am wondering if the maf column is necessary for mtag? I did not find any flag to avoid using maf.

Best, Ming

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chenming9453 commented 4 years ago

Thank you for your prompt response! And Thank you for the solution.

Best, Ming

divbru commented 1 year ago

Hi, does the --eaf_name require MAF or the effect allele (a1) frequency ? The tutorial refers to EAF while the manual (./mtag.py -h) refers to the MAF. Thank you!

paturley commented 1 year ago

Ah! Thanks for catching the discrepancy. It should be the effect allele frequency.

On Tue, Mar 7, 2023 at 2:38 AM Divya @.***> wrote:

Hi, does the --eaf_name require MAF or the effect allele (a1) frequency ? The tutorial refers to EAF while the manual (./mtag.py -h) refers to the MAF. Thank you!

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